4-786557-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006651.4(CPLX1):c.349C>T(p.Leu117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,609,214 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00017 ( 2 hom. )
Consequence
CPLX1
NM_006651.4 synonymous
NM_006651.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.63
Genes affected
CPLX1 (HGNC:2309): (complexin 1) Proteins encoded by the complexin/synaphin gene family are cytosolic proteins that function in synaptic vesicle exocytosis. These proteins bind syntaxin, part of the SNAP receptor. The protein product of this gene binds to the SNAP receptor complex and disrupts it, allowing transmitter release. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 4-786557-G-A is Benign according to our data. Variant chr4-786557-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 790827.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.63 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPLX1 | NM_006651.4 | c.349C>T | p.Leu117= | synonymous_variant | 4/4 | ENST00000304062.11 | |
CPLX1 | XM_011513391.2 | c.304C>T | p.Leu102= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPLX1 | ENST00000304062.11 | c.349C>T | p.Leu117= | synonymous_variant | 4/4 | 1 | NM_006651.4 | P1 | |
CPLX1 | ENST00000505203.1 | c.286C>T | p.Leu96= | synonymous_variant | 5/5 | 2 | |||
CPLX1 | ENST00000504062.1 | c.304C>T | p.Leu102= | synonymous_variant | 3/3 | 3 | |||
CPLX1 | ENST00000506404.1 | n.402C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152070Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000195 AC: 47AN: 240688Hom.: 1 AF XY: 0.000214 AC XY: 28AN XY: 130832
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GnomAD4 exome AF: 0.000166 AC: 242AN: 1457030Hom.: 2 Cov.: 36 AF XY: 0.000192 AC XY: 139AN XY: 724454
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74394
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2023 | - - |
CPLX1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at